Stargate SG-1: Project Chronarch
by The TARDIS Courier
Summary: After a close call with the Goa'uld SG-1 will have to team up with a complete stranger in the fight for survival OCxOC Warning!: this story does not contain any of the cannon Doctors, this is my own Doctor with his own back story. only read this if you want to, not if you expect grumpy, bow-tie or sandshoes.


Courier: hello everyone here is an idea that springs in my head every time I watch Stargate and after many different variations I have finally made an intro I like

Please favourite and leave your opinions in the review section

goa'uld _**"Jaffa Kree!"**_

This story also takes place beginning of season 3 between Seth and Fair game, the story will begin to follow the series by chapter three

Stargate SG-1

Project: Chronarch

Episode 1: Invasion

It was a quite night for the SGC, no intergalactic conflicts, no life threatening situations just a calm evening for SG-1 and the rest of the human race.

**Sam's Workshop**

Captain Samantha Carter was one of those people that had tons of things to keep her occupied, though she enjoyed working on scientific projects she loved spending a good few hours on her motorcycle but normally she would have her radio on full volume however Jack had knocked over her radio the last time she was working on her bike and it never worked since, she didn't mind working in silence but the whole point of the radio was to avoid her from being distracted but for some reason she found it hard to concentrate in complete silence. As she was working on the forks from her front suspension she heard a very odd sound coming done the hall way, she had stopped and paused, she had heard it before it was a wheezing noise, slow metallic. As the noise got louder the emergency alarm sounded along with the voice of Sgt Walter in the intercom.

"Emergency! Unknown entity in the gate room, SG-1 and General Hammond to the control room" Sam had dropped her tools and ran in response to the emergency, while she ran she noticed that Walter didn't say that the gate was active, maybe it was the asgard or a race that had similar teleportation Technology, she would know sooner when she arrived and when she did she stood in shock, standing in front of the Stargate was a 10 foot tall blue police box and by the look of it had been through hell, smashed and cracked windows, scorching all over the wooden surface and the top light was hanging on by the wiring as it stopped flashing, though it looked harmless the security for the gate room had their weapons pointed at the box each with blank and confused looks on their faces. Running up behind her was Colonel Jack O'Neill and Teal'c who where both in training gear from the sparing match the where having, General Hammond and Dr Daniel Jackson had also arrived in the control room.

"Carter any idea what it is?" Jack asked catching his breath.

"No idea sir, I just got here myself" Sam replied not taking her eyes of the box.

"It appears to be a phone booth used by the British in the country of UK" Teal'c commented and funnily enough he was correct.

"That's the UK and the correct term is Britain or England, it's only called the UK if it involves Northern Ireland" Teal'c responded to Jacks explanation with a raised eyebrow.

"But what's it doing here? Better question is how?" Sam questioned before she noticed the door to the phone box begin to open. With the soldiers facing the door noticing it as well they raised their weapons ready to make the occupant a display of Swiss cheese. As the door opened fully a cloud of smoke erupted from the box, as it cleared a boy in his late teens to early twenties wearing a grey T-shirt, blue jeans and a long black trench coat could be seen leaning against the now closed door of the box, though he looked exhausted he stood up and blew away the smoke having a look around not going any further due to the mass of guns pointed at his head, before one of them could kill him Hammond had prevented them from attacking.

"Hold your fire!"

"Ooh guns how lovely, I must be on earth" as the boy moved Sam noticed that he was stumbling and was struggling to keep up "and what's that…" The boy said pushing past the soldiers and up the grated ramp towards the gate "a Stargate! You use this thing how adorable, I remember building a portable one of these for my first science project got a F, mind you they were incredibly basic" the boy was spinning all over the place like he was just out drinking when he began to walk backwards he didn't notice the handrail behind him.

"Hey watch out for the…" Sam called out but it was too late, he had tripped and fallen hard on the concrete ground, surprisingly however he got straight back up.

"I'm fine! I am fine! 100 percent A-okay" as he stumbled back to the box he came out off Hammond had called for medical care. The boy was still looking around but stopped when he saw Sam still staring.

"Hello" he said with a gentle smile "I'm The Doctor" then the boy collapsed just as Dr Fraiser had arrived.

"Colonel who is this?" Janet Fraiser asked as she attended to the collapsed stranger.

"No idea, all he did was rant but he did say he was a doctor" Jack answered while Janet checked his vitals.

"Well whoever he is he as dangerously abnormal heart beat; we need to get him to the infirmary NOW!" SG-1 then ran to assist getting the boy on a stretcher and transporting him to the base's infirmary.

**Infirmary**

As Dr Fraiser, SG-1 and Hammond arrived in infirmary, Teal'c using his Jaffa enhanced strength to lift the stranger onto one of the medical beds followed by Janet strapping him to a heart monitor but when she turned it on the three doctors in the room stared at the readings like looking at the impossible.

"Am I seeing that correctly" Dr Daniel Jackson asked pointing at the heart monitor.

"How is that possible, Janet?" Sam asked while Janet stood staring at the stranger rather than the machine.

"None, at that heart rate he should be dead" Janet then went for a sedative to lower his heart rate but when she was next to him as soon as she tested the needle the boy inhaled deeply before his eyes shot open and grabbed Janet's arm before she could inject him, using great strength he grabbed her lab coat and pulled he close to whisper in her ear.

"I'm not human, test the blood" as Jack pulled Janet away the boy fell back into unconsciousness with his heart rate unchanged.

"Doc you alright" Jack said as Teal'c pulled a zat gun in case the boy would get up again.

"Yes Colonel I'm okay, however he asked me to test his blood, General?" looking to Hammond for approval he gave a simple nod prompting Teal'c to point the zat gun at point blank range so he would not miss. As Janet pulled a needle full of blood she looked at it with a troubled face "Sir, I suggest until I have completed my analysis of this man's blood we leave him be" Hammond looked at his chief medical officer then back to the unconscious boy.

"Very well, I'll leave you to it, Teal'c keep an eye on him, I want a full briefing as soon asap doctor" Hammons said agreeing with Dr Fraiser.

"What about his heart rate, won't he die?" Daniel asked just as the general left.

"I don't think he wills Daniel, no one with that heart rate could live for more than a few minutes and his body isn't reacting in a way a person would. If he does show signs of heart failure I'll do everything I can to help him but according to him he isn't human" not exactly satisfied Daniel left along with Sam to have a look at that box and Jack looked at the guy who was supposedly a doctor and looking at his clothes he noticed they where to big and were covered with dry blood.

"This kids dressed like he's been through hell and back but he hasn't got a scratch" as Jack looked at his alien friend he too inspected the young man.

"Indeed" Teal'c said before Jack went to talk to Sam.

**Gate Room**

When Jack arrived to the gate room Sam was already scanning the box for any form of energy readings or radiation while Daniel was just staring at it.

"So Daniel…anything?" Daniel looked at his best friend then back to the box with a stumped look.

"If it was anything else I might but I just can't figure out why a person claiming to be alien would fall out of a police box from 1950's London" realising Daniel had nothing Jack turned to the only person he could.

"Carter…Anything" Sam stopped scanning the box and looked back to her commanding officer.

"Well sir apart from normal readings nothing much just a form of energy I've never seen before" Sam reported looking at the laptop she set up.

"Well you ponder that while I go for some lunch".

**Few hours later in the briefing room**

"So doctor what have you got?" Hammond asked Dr Fraiser as she passed down folders.

"Well he was telling the truth he isn't human and despite his appearance he is very much different to us, after running basic blood test I found that he has triple helix DNA" This shocked Sam on a scientific stand point, DNA were the building blocks of the universe a species having a triple helix was definitely unique.

"English doc" Jack said not understanding what she was going on about.

"DNA in a physical form has a double helix structure, every species we have encountered and have tested DNA for all have a double helix this is the first I've encountered someone with otherwise" Janet explained not helping Jacks confusion at all.

"So what does that mean?"Daniel asked having a limited knowledge of DNA only able to understand the basics.

"I don't know, it could potentially mean anything" Janet replied.

"What about the boy's unusual heart rate?" Teal'c asked to which Janet pulled out a sonar reading.

"Unsure of how he would react to X-rays, I used sonar instead and discovered he has two hearts" everyone in the room was intrigued.

"Really?" Sam asked in astonishment looking at the sonar image which clearly showed two hearts one on each side of his torso.

"Yes and two livers as well, General this boy is a medical wonder, he looks human, sounds humans but he is far more equipped than us, there is no telling what kinds of biological differences he has compared to us" Janet explained in wonder but was halted by the activation of the Stargate followed by Walters voice.

"Unscheduled off-world activation" as soon as Walter finished SG-1, Dr Fraiser and Hammond all descended to the control room.

"Do we have an IDC sergeant?" Hammond asked Walter as he waited for a confirmation.

"Yes sir we do, SG-7" as the screen flashed green signalling a correct access code Hammond gave the order.

"Open the iris"

**Infirmary**

As the young man lay peacefully under the watchful eye of the nurses, they failed to notice that when he exhaled every now and again gold vapour floated outwards and immediately disappeared.

**Control room**

As the iris opened SG-1, Dr Fraiser and the General expected to see a group of men walk though and relax after a long day but instead a round ball-like device rolled through and was immediately recognised by SG-1 but flashed brightly before they could react. After the light dimmed everyone in the gate and the control room had collapsed and coming through the Stargate were men full clad in armour with bird like helmets after a small group had came through the gate another wearing the same armour without the helmet came through, he was a white male with short black hair and a gold mark on his head in the shape of a bird.

"_**JAFFA KREE!"**_ as the Jaffa in charge shouted his orders the rest of the Jaffa spread out dragging the bodies of the SGC personnel away, the Jaffa with the gold mark noticed in his immediate field of view was a large wooden box stepping back out of fear before taking out a grey orb which revealed the face of a man who looked in his early thirty's and shaved bald "my lord Heru'ur we have taken the Tau'ri base however I have discovered that he is here the Chronarch" the sound of that name made the eyes of the man known as Heru'ur widen in fear but only for a brief moment.

"Find him and destroy him! Do not fail me first prime" as Heru'ur gave his command his faced disappeared and the First Prime to Heru'ur began his search for the owner of the box.

**Infirmary**

Instead of killing everyone in the base, the Jaffa instead stunned them in order to avoid conflict and to allow their god to signal handily kill them himself. As a Jaffa soldier had entered the infirmary he looked around and noticed that the bed closest to him was recently occupied, walking closer to investigate he tensed up and fell to the ground after being shocked by the previously unconscious man, he then raised the defibrillator he used as a weapon to his mouth blowing hit like a smoking gun.

"Clear" the man then picked up the staff weapon and left the infirmary.

**Storage room**

Sam woke up with a major head ache looking around to see a good portion of the base's personnel present then memories flooded back in and she realised that the base was under attack, beside her was Jack also waking up with a nasty head ache, he however remembered form the start.

"Carter please tell me I was dreaming of a goa'uld grenade rolling out of the gate?" Jack asked Sam giving him a half hearted smile.

"Sorry sir" she said has Jack hit his head purposefully on the ground.

"Dam" he said to himself as he got up "where's Teal'c and Daniel?"

"I don't know, they must have separated us knowing we work better all together" as she spoke other people began to wake up just as the door opened with a Jaffa soldier walking through with two more standing guard.

"You!" the Jaffa spoke with an disgusted tone at Sam after pointing at her one of the two guarding the door walked over to the two members of SG-1 and grabbed Sam only for Jack to intervene but was thrown against the wall. As the Jaffa grabbed Sam again the sound of a staff weapon was heard from the door as the guard standing their fell to the ground dead "Jaffa Kree!" the Jaffa holding Sam let go moving to investigate the disturbance but as he turned the corner was forced back after being hit by the end of a staff weapon after falling to the ground a young man entered the room and pointed the staff weapon he was holding at the only remaining Jaffa.

"_**Bet Jaffa!" **_the young man called out speaking in perfect goa'uld.

"_**Kree Tal Shal Mak!" **_the Jaffa retaliated.

"_**Metak Shatak Oz!" **_the man spoke again before pulling out a zat gun and stunning him, he then looked around and began to address the room this, time in English "ok everyone listen up, your base is currently under process of invasion so to make things simple, I ask you to stay here while I clean house" as most of the people didn't say a word, he did just take out three Jaffa easily so no one objected well almost no one.

"And who the hell are you!" Jack yelled getting up after he was shoved aside but the man in response just left the room with Sam and jack following "hey! I'm taking to you"

"And I don't care" The man relied as he turned to enter one of the armoury's opening the door with a blank key card, he then pulled out two vests and two P-90 SMG's "here, make yourselves useful if you're going to follow me around"

"What make you think we're going to follow you?" Jack said to the man as he equipped a holsters to his legs for two pistols and a shotgun strapping it to his back along with several boxes of ammo for each weapon, shoving them in his pockets surprising Sam as they showed no signed of anything thing in them despite one pocket being filled with three boxes of shotgun shells.

"I didn't say you had to follow me in combat, I just know you're going to follow where ever I go and where I'm going is where I'm going to take back this base. So you coming or not?" without saying another word Jack cocked his weapon ready to fight along with Sam "Sweet, now Avanti!" both SG-1 members looked at the man with a raised eyebrow at his choice of words "what? It means onwards in Italian"

As the three traversed the base Sam was thinking of questions to ask the stranger but she could only think of the basics.

"So, what do we call you?" the young man looked back to Sam.

"I already told you didn't i?" he replied.

"No, no you didn't all you said was you're a doctor" Jack followed making the boy stop and look at the veteran airman.

"No I said I was 'The' Doctor Note the _'The'_" the boy said before continuing.

"Okay then 'The Doctor' what's the plan?" Jack asked realising he will need his help in taking back the base.

"Ok to be clear only refer to me as The Doctor when talking about me, when talking to me call me Doctor and the plan is he disable the Stargate and purge hostiles" The Doctor said lifting his staff weapon as he said the word purge.

"Disable the Stargate?" Sam asked wondering why.

"Well if we disable the gate then the bad guys can't leave and it will allow us to leave the gate unattended, one of you guys knows how to do that right?" The Doctor explained then asked.

"I can but we will have a better fighting chance with the rest of the team" Sam noted followed by The Doctor giving the Captain a smile before leaping across hall T-junction to the other side as a flurry of staff weapon fire could be heard from behind the corner.

"I count two hostiles, cover your ears!" The Doctor shouted over before bringing out a grenade and throwing it down the hall way, after a couple of second the explosion rang though Sam's ears and the Jaffa had stopped firing. Looking around the corner both Jaffa where on the ground killed by the shock wave of the grenades.

"Nice" Jack approved as he turned the corner and checked for any more Jaffa troops.

"now I thing the other two are in here" The Doctor said as he opened the door, on a chair hand bound was Teal'c as the free Jaffa looked up expecting to see followers of Heru'ur he instead say his friends and the alien who had arrived in the box.

"O'Neill, Captain Carter it is good to see you" as Jack went to untie Teal'c the Doctor pulled out a silver and black stick shaped device pointed it at Teal'c and pressed a small button on the side lighting up a blue point and making a high-pitched buzzing sound, in result the rope tying Teal'c simply fell off stunning the three members of SG-1.

"Nifty gadget" Jack said as The Doctor put the device back in his pocket.

"Sonic screwdriver, never leave home without it" The Doctor then passed the staff weapon to Teal'c who caught it while standing up "tell you want, a Jaffa is a bold choice for an ally"

"He has his moments" Jack said with a smile before the group when to look of Daniel.

**Control Room**

As Daniel woke up from his daze he was greeted with a smack by the first Prime of Heru'ur.

"Ow" Daniel said containing the pain.

"Tell me where the he is and I will spare your life" the Jaffa demanded.

"And who is he?" Daniel replied not knowing who the Jaffa was on about.

"The Chronarch" the name was interesting but the only person he could think of was the boy with the box.

"I'm afraid I have no idea what you are talking about" Daniel claimed half true but like most the Jaffa failed to listen to the truth.

"You will tell me where he is or this one dies" the Jaffa threatened pointing his staff weapon at Janet who was still unconscious, Daniel also spotted Hammond beside Janet also unconscious.

"I don't even know what a Chronarch is let alone where one is" not receiving the answer he desired only angered the Jaffa instead of listening.

"YOU LIE! Where is the Chronarch!" as he continued to demand he felt a small poke on his shoulder as he turned he say a young male with short brown hair and wearing a black trench coat.

"Sup" he said before sucker-punching him knocking him out cold "oww that guy's head is like a rock" as The Doctor complained Sam, Jack and Teal'c entered the control room and helped Daniel up.

"Are you unharmed Daniel Jackson?" Teal'c asked concerned for his friend.

"Yes I'm fine just a couple of bruises for tomorrow" after answering Teal'c Daniel began to stare at The Doctor who was standing in front of him.

"Could you stop staring at me? It's creepy" The Doctor asked disturbed by Daniels fascination.

"I'm sorry I didn't mean to stare, I'm Dr Daniel…"

"Jackson, yes I know who you are I read your book, very intriguing yet still humanity fails to see the truth beyond Myth" The Doctor interrupted surprising to Daniel that he knew who he was "I'm The Doctor" The Doctor introduced holding out his hand which Daniel took in good faith.

"Doctor? Doctor of what?" Daniel asked confused about his name.

"Just that, call me The Doctor" he explained rather vaguely.

"Now that we have a minute, mind telling us a bit more than The Doctor?" Jack asked since the First prime was down and the rest of the Jaffa weren't going to kill the prisoners .

"What is there to tell, better question is what do you want to know?" The Doctor asked ready for some questions to avoid more.

"Where are you from?" Daniel asked.

"Gallifrey" he replied without hesitation.

"And I'm guessing you are a Chronarch" Daniel asked again referencing what The Jaffa was looking for.

"Close that's what middle class species call me the actual name is Time Lord" he corrected.

"Bit boastful don't you think" Jack retorted.

"Yea kind of a traditional thing but accurate none the less" The Doctor said showing his own feelings about the name of his race.

"Why where you acting like you were in the gate room you seem much more controlled unlike the last time" Sam asked.

"Well I had just regenerated and since for Time Lords driving after regenerating is like driving while drunk and so I aimed the Tardis to crash somewhere on earth, sorry about the her by the way I'll move her aside later" he explained casually.

"Regenerated?" Daniel and Sam both said at the same but before The Doctor could answer he keeled over, looking like he was about to barf he coughed up a small cloud of golden energy, which Jack and Teal'c reacted by raising their weapons.

"Don't worry it isn't dangerous, just excess energy. You see I while ago I was killed. Regeneration is my peoples way for healing and I had just gone through the process when I crashed in exchange for the fix up, my appeared changed and judging by my voice I'm a lot younger" The Doctor Explained while getting up.

"Your appearance?" Sam asked in confusion.

"Yea, it's a bit difficult to explain on the fly but think of it this way. Imagine I was him" he said pointing at Jack "then during the process of regeneration, my body is repaired but then I become him" the continued now pointing at Daniel "My body completely changes along with my personality with my memories being the only thing that remains even then it gets scrambled like eggs in a blender every time" The complete group of SG-1 looked in disbelief in the young alien while he turned on the spot and activated the base's intercom "right, time to put on a show" having a little cough preparing his voice he began to address the entire base "attention all idiots wearing stupid armour, your leader the one with the gold thing on his head has been put down, so I give this waning surrender know and I will let you leave unharmed, if you agree to my terms allow one of the humans to tell me so otherwise I will activate the self destruct and trust me i will survive, there is a reason why your gods call me the Destroyer. That is all" after The Doctors speech the entire base was dead quite with only the beeps and clicks of the equipment in the gate room.

"Again a bit boastful" Jack joked again while The Doctor tuned back.

"You think, I was going to use the I'm a Time Lord speech, I do love that one but these twits don't even know what I Time Lord is" The Doctor then looked at the rebel Jaffa "no offence their big man" Teal'c then turned his head slightly then turned back.

"None taken" just as they began to relax for a moment the phone began to ring as The Doctor picked it up Walter began relaying the Jaffa's choice.

"Hello"

"Uh hello, the Jaffa are standing down and are being escorted to the holding cells" Walter explained to the stranger that disarmed an entire militia of Jaffa with only his words.

"No bring them to the Stargate, I'm a man of my word and I can get…uh O'Neill, yea O'Neill to tell you instead"

"Ok sir, we'll bring them up" as The Doctor put the phone down SG-1 began to question his decision.

"Why are you letting them go?" Daniel asked on behalf of the team.

"Because then I would be better than them plus they surrendered in exchange for their freedom, it just seems wrong to go against my word" as he finished Dr Fraiser and General Hammond began to stir and wake up.

"But we can't send them back he don't have the address they came from" Sam commented which The Doctor answered by taking out his Device known as a sonic screwdriver and flipping it I his hand, he then flicked it making it extend with four claws, pointing it at the Stargate he pressed the button and after the tip lit up and the bussing sound blared the gate instantly activated and opened.

"Instant return, every Stargate stores the last known address it connected to useful trick if you need to follow someone" the members of SG-1 all smiled at the brilliance of their new ally.

"Does someone mind telling me what's going on?" Hammond asked after regaining all his sense.

"Well George it's a long story" Jack said as the first of the Jaffa began to enter the gate room.

**An hour and a detailed explanation later**

As the last of the Jaffa were escorted back to where they came from, SG-1 were told that the entirety of SG-7 had been executed by Heru'ur and as The Doctor and Teal'c watched as the only killed Jaffa where stretchered threw the gate in good faith one airman was walking the first prime to the gate ready to send him back but he was stopped by The Doctor.

"Not him he can stay" with a nod from Teal'c the airman began to escort the Jaffa to the holding cells. After the gate was deactivated the rest of SG-1, Dr Fraiser and General Hammond entered the gate room.

"Doctor on behalf of this facility and ever soul in it I thank you for your help" General Hammond thanked the Time Lord with a salute which The Doctor returned with a more casual version.

"Not a problem General, just be glad I woke up when I did or I would have been captured and the SGC would have been overrun" despite the cheerful smile he had The Doctor began to feel very faint and as quickly has he shut his eyes he collapsed once again.

**Infirmary, 10 hours later**

Opening his eyes The Doctor could see he was back in the bed he started in and looking around he saw Sam at his side who had fallen asleep, as The Doctor tried to get up Sam began to stir and lifted her head realising where she had fallen asleep.

"Morning sleepy head" The Doctor joked as she blushed in embarrassment.

"Sorry, didn't think I'd dose off" Sam apologised which The Doctor rasied his hand to stop her.

"It's not a problem you've had a rough day, why don't you go and get some sleep" agreeing with him Sam got up with a smile and began to leave the infirmary but she was halted by The Doctor as he called out "by the way I didn't catch your name"

"Its Sam, Samantha Carter" she replied keeping her smile.

"Nice to meet you Sam" and after a proper greeting she left the Doctor as he began to drift off, knowing that his regeneration cycle had completed.

**Next Episode:**

**New Adjustment**

Courier: huh pretty good right. Of course it was, took some doing but I got there

As for my other series Doctor Who: Equestrian Chronicles by the time you've read this I would be around finishing it and that will tie up Season 1 then a charismas special.

After which I'll begin work on season two hitting it off with everyone's favourite draconian (Discord if you have no idea what a draconian is)

This series will also run alongside the other but from past experiences it will be quite a bit from each episode but remember be patient and you will get your fill

Have fun guys and keep reading

Avanti!


End file.
